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When running Queue jobs locally, merge the stderr to the stdout log if the error file is NOT specified. 

Updated VE strats in the HSP for plotting Ka/Ks by AC.
This commit is contained in:
Khalid Shakir 2012-01-10 16:10:25 -05:00
parent dc60757b68
commit ef50e77ee2
1 changed files with 3 additions and 3 deletions
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6
public/scala/src/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala
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@ -1,5 +1,5 @@
/* /*
* Copyright (c) 2011, The Broad Institute * Copyright (c) 2012, The Broad Institute
* *
* Permission is hereby granted, free of charge, to any person * Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation * obtaining a copy of this software and associated documentation
@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.runtime.{ProcessSettings, OutputStreamSett
/** /**
* Runs jobs one at a time locally * Runs jobs one at a time locally
* @param function Command to run.
*/ */
class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRunner { class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRunner {
// Controller on the thread that started the job // Controller on the thread that started the job
@ -39,13 +40,12 @@ class ShellJobRunner(val function: CommandLineFunction) extends CommandLineJobRu
/** /**
* Runs the function on the local shell. * Runs the function on the local shell.
* @param function Command to run.
*/ */
def start() { def start() {
val commandLine = Array("sh", jobScript.getAbsolutePath) val commandLine = Array("sh", jobScript.getAbsolutePath)
val stdoutSettings = new OutputStreamSettings val stdoutSettings = new OutputStreamSettings
val stderrSettings = new OutputStreamSettings val stderrSettings = new OutputStreamSettings
val mergeError = (function.jobErrorFile != null) val mergeError = (function.jobErrorFile == null)
stdoutSettings.setOutputFile(function.jobOutputFile, true) stdoutSettings.setOutputFile(function.jobOutputFile, true)
if (function.jobErrorFile != null) if (function.jobErrorFile != null)